Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014398.1 Corchorus capsularis cultivar CVL-1 contig14419, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55084
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1839 original size:105 final size:105
Alignment explanation
Indices: 1657--1868 Score: 415
Period size: 105 Copynumber: 2.0 Consensus size: 105
1647 TCTTACCACA
1657 TTATTATTATTTCATAATAATGTAACGTTAATTTAATAAGCATTTACTATGTTGCATGGCATTGC
1 TTATTATTATTTCATAATAATGTAACGTTAATTTAATAAGCATTTACTATGTTGCATGGCATTGC
*
1722 AAGCGATTTTAAAAGTTTTAAGAGCTTCAATCGCTTGCAC
66 AAGCGATTTTAAAAGTTTTAAGAGCATCAATCGCTTGCAC
1762 TTATTATTATTTCATAATAATGTAACGTTAATTTAATAAGCATTTACTATGTTGCATGGCATTGC
1 TTATTATTATTTCATAATAATGTAACGTTAATTTAATAAGCATTTACTATGTTGCATGGCATTGC
1827 AAGCGATTTTAAAAGTTTTAAGAGCATCAATCGCTTGCAC
66 AAGCGATTTTAAAAGTTTTAAGAGCATCAATCGCTTGCAC
1867 TT
1 TT
1869 TCGTTGTGGA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (105 bp):
TTATTATTATTTCATAATAATGTAACGTTAATTTAATAAGCATTTACTATGTTGCATGGCATTGC
AAGCGATTTTAAAAGTTTTAAGAGCATCAATCGCTTGCAC
Found at i:4220 original size:41 final size:41
Alignment explanation
Indices: 4163--4285 Score: 237
Period size: 41 Copynumber: 3.0 Consensus size: 41
4153 CCGAAACAAA
*
4163 AGAAACTCTTCTAGTAACAACTCTGTCCGACAAATCAGATT
1 AGAAACTCCTCTAGTAACAACTCTGTCCGACAAATCAGATT
4204 AGAAACTCCTCTAGTAACAACTCTGTCCGACAAATCAGATT
1 AGAAACTCCTCTAGTAACAACTCTGTCCGACAAATCAGATT
4245 AGAAACTCCTCTAGTAACAACTCTGTCCGACAAATCAGATT
1 AGAAACTCCTCTAGTAACAACTCTGTCCGACAAATCAGATT
4286 GAAGAAGAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (41 bp):
AGAAACTCCTCTAGTAACAACTCTGTCCGACAAATCAGATT
Found at i:8351 original size:15 final size:15
Alignment explanation
Indices: 8317--8364 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
8307 ATAATTGCTA
* *
8317 TCATTTTGAAATGAT
1 TCATTTTAAAATGTT
*
8332 GCATTTTAAAATGTT
1 TCATTTTAAAATGTT
8347 TCATTTCTAAAAT-TT
1 TCATTT-TAAAATGTT
8362 TCA
1 TCA
8365 GACTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (15 bp):
TCATTTTAAAATGTT
Found at i:8556 original size:2 final size:2
Alignment explanation
Indices: 8524--8548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8514 ACACACACAG
8524 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8549 ACATATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15413 original size:19 final size:18
Alignment explanation
Indices: 15370--15417 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
15360 AAAAAAAAAA
*
15370 ATATATATATAATTATTT
1 ATATATATATAATTATTC
15388 ATA-ATATATTAATATATCTC
1 ATATATATA-TAAT-TAT-TC
15408 ATATATATAT
1 ATATATATAT
15418 TATCTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 7 0.28
19 3 0.12
20 5 0.20
21 5 0.20
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATATAATTATTC
Found at i:15415 original size:21 final size:19
Alignment explanation
Indices: 15370--15419 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
15360 AAAAAAAAAA
*
15370 ATATATATA-TAATTATTT
1 ATATATATATTAATTATTC
15388 ATA-ATATATTAATATATCTC
1 ATATATATATTAAT-TAT-TC
15408 ATATATATATTA
1 ATATATATATTA
15420 TCTGAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.19
18 7 0.26
19 3 0.11
20 4 0.15
21 8 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATATATTAATTATTC
Found at i:17446 original size:14 final size:14
Alignment explanation
Indices: 17429--17457 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17419 CCAAAATAAA
17429 AACCGAAAAAACCG
1 AACCGAAAAAACCG
17443 AACCGAAAAAACCG
1 AACCGAAAAAACCG
17457 A
1 A
17458 CATTGACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.28, G:0.14, T:0.00
Consensus pattern (14 bp):
AACCGAAAAAACCG
Found at i:20083 original size:32 final size:32
Alignment explanation
Indices: 20042--20106 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20032 TACACTTACA
20042 TTTTCATGTGGCTCTTAGTTTATTCTTTGTGC
1 TTTTCATGTGGCTCTTAGTTTATTCTTTGTGC
20074 TTTTCATGTGGCTCTTAGTTTATTCTTTGTGC
1 TTTTCATGTGGCTCTTAGTTTATTCTTTGTGC
20106 T
1 T
20107 ACATTGGCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.09, C:0.15, G:0.18, T:0.57
Consensus pattern (32 bp):
TTTTCATGTGGCTCTTAGTTTATTCTTTGTGC
Found at i:25116 original size:13 final size:14
Alignment explanation
Indices: 25098--25127 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25088 TTTTTCTTAC
25098 ATTAATTAAT-ATA
1 ATTAATTAATAATA
25111 ATTAATTAATAATA
1 ATTAATTAATAATA
25125 ATT
1 ATT
25128 CATTGTCCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTAATTAATAATA
Found at i:25215 original size:15 final size:15
Alignment explanation
Indices: 25195--25247 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
25185 TCTTATTCTC
25195 ATTATTATA-ATAAAT
1 ATTATTATATAT-AAT
*
25210 ATTATTATATATATT
1 ATTATTATATATAAT
*
25225 ATTATTATTATATACT
1 ATTATTA-TATATAAT
25241 ATT-TTAT
1 ATTATTAT
25248 TACTACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 1 0.03
15 21 0.62
16 12 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATATATAAT
Found at i:25230 original size:18 final size:18
Alignment explanation
Indices: 25209--25249 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
25199 TTATAATAAA
25209 TATTATTATATA-TATTAT
1 TATTATTATATACTATT-T
25227 TATTATTATATACTATTT
1 TATTATTATATACTATTT
25245 TATTA
1 TATTA
25250 CTACTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATTATATACTATTT
Found at i:25235 original size:21 final size:21
Alignment explanation
Indices: 25210--25249 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25200 TATAATAAAT
25210 ATTATTATA-TATATTATTATT
1 ATTA-TATACTATATTATTATT
*
25231 ATTATATACTATTTTATTA
1 ATTATATACTATATTATTA
25250 CTACTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTATATACTATATTATTATT
Found at i:27174 original size:20 final size:20
Alignment explanation
Indices: 27149--27194 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
27139 TTTAGTCAAT
27149 GGGTTTTAACCGGGTCGAAC
1 GGGTTTTAACCGGGTCGAAC
27169 GGGTTTTAACCGGGTCGAAC
1 GGGTTTTAACCGGGTCGAAC
27189 GGGTTT
1 GGGTTT
27195 CAAGTTCCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.37, T:0.28
Consensus pattern (20 bp):
GGGTTTTAACCGGGTCGAAC
Found at i:27719 original size:30 final size:30
Alignment explanation
Indices: 27683--27741 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
27673 GCTATTCTTA
* * *
27683 TGAATAACAAAATAGTCAAATTTGTGGATT
1 TGAATAAAAAAAAAGTCAAATATGTGGATT
27713 TGAATAAAAAAAAAGTCAAATATGTGGAT
1 TGAATAAAAAAAAAGTCAAATATGTGGAT
27742 ATGTGCGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (30 bp):
TGAATAAAAAAAAAGTCAAATATGTGGATT
Found at i:34013 original size:12 final size:12
Alignment explanation
Indices: 33998--34033 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
33988 TAAATGTCTT
*
33998 TTTTATTTTTTA
1 TTTTAATTTTTA
*
34010 TTTTAATATTTA
1 TTTTAATTTTTA
34022 TTTTAATTTTTA
1 TTTTAATTTTTA
34034 ATATTTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTAATTTTTA
Found at i:34021 original size:19 final size:19
Alignment explanation
Indices: 33999--34055 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
33989 AAATGTCTTT
33999 TTTATTTTTTATTTTAATA
1 TTTATTTTTTATTTTAATA
*
34018 TTTA-TTTTAATTTTTAATA
1 TTTATTTTTTA-TTTTAATA
*
34037 TTT-TTTGTTTATTTAAATA
1 TTTATTT-TTTATTTTAATA
34056 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.16
19 24 0.75
20 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATTTTTTATTTTAATA
Found at i:49253 original size:26 final size:27
Alignment explanation
Indices: 49224--49274 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
49214 TCTAAAAGTT
49224 ATATA-TGAATTATAGAAAAACCAATC
1 ATATAGTGAATTATAGAAAAACCAATC
*
49250 ATATAGTTAATTATAGAAAAACCAA
1 ATATAGTGAATTATAGAAAAACCAA
49275 GCGGCCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (27 bp):
ATATAGTGAATTATAGAAAAACCAATC
Done.